Growing interest in the development of innovative functional products as ideal carriers for synbiotics, e.g., nutrient bars, yogurt, chocolate, juice, ice cream, and cheese, to ensure the daily intake of probiotics and prebiotics, which are needed to maintain a healthy gut microbiota and overall well-being, is undeniable and inevitable. This review focuses on the modern approaches that are currently being developed to modulate the gut microbiota, with an emphasis on the health benefits mediated by co-encapsulated synbiotics and immobilized probiotics. The impact of processing, storage, and simulated gastrointestinal conditions on the viability and bioactivity of probiotics together with prebiotics such as omega-3 polyunsaturated fatty acids, phytochemicals, and dietary fibers using various delivery systems are considered. Despite the proven biological properties of synbiotics, research in this area needs to be focused on the proper selection of probiotic strains, their prebiotic counterparts, and delivery systems to avoid suppression of their synergistic or complementary effect on human health. Future directions should lead to the development of functional food products containing stable synbiotics tailored for different age groups or specifically designed to fulfill the needs of adjuvant therapy.